diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 6c6299833a3..b7d512dc724 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,209 +1,216 @@ ---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" -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" -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" -appdirs==1.4.4 ; python_version >= "3.7" and python_version < "3.12" -arcp==0.2.1 ; python_version >= "3.7" and python_version < "3.12" -argcomplete==3.1.1 ; python_version >= "3.7" and python_version < "3.12" -async-timeout==4.0.3 ; python_version >= "3.7" and python_version < "3.12" -asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8" -attmap==0.13.2 ; python_version >= "3.7" and python_version < "3.12" -attrs==23.1.0 ; python_version >= "3.7" and python_version < "3.12" -babel==2.12.1 ; python_version >= "3.7" and python_version < "3.12" -backports-zoneinfo==0.2.1 ; python_version >= "3.7" and python_version < "3.9" -bagit-profile==1.3.1 ; python_version >= "3.7" and python_version < "3.12" -bagit==1.8.1 ; python_version >= "3.7" and python_version < "3.12" -bcrypt==4.0.1 ; python_version >= "3.7" and python_version < "3.12" -bdbag==1.7.1 ; python_version >= "3.7" and python_version < "3.12" -beaker==1.12.1 ; python_version >= "3.7" and python_version < "3.12" -billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.12" -bioblend==1.2.0 ; python_version >= "3.7" and python_version < "3.12" -bleach==6.0.0 ; python_version >= "3.7" and python_version < "3.12" -boltons==23.0.0 ; python_version >= "3.7" and python_version < "3.12" -boto==2.49.0 ; python_version >= "3.7" and python_version < "3.12" -botocore==1.27.59 ; python_version >= "3.7" and python_version < "3.12" -bx-python==0.10.0 ; 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" -certifi==2023.7.22 ; python_version >= "3.7" and python_version < "3.12" -cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12" -charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12" -cheetah3==3.2.6.post1 ; python_version >= "3.7" and python_version < "3.12" -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" -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" -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" -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" -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" -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" -fastapi-utils @ git+https://github.com/mvdbeek/fastapi-utils@pydantic-2; python_version >= "3.7" and python_version < "3.12" -fastapi==0.101.0 ; python_version >= "3.7" and python_version < "3.12" -filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.12" -frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12" -fs==2.4.16 ; python_version >= "3.7" and python_version < "3.12" -fsspec==2023.1.0 ; python_version >= "3.7" and python_version < "3.12" -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" -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" -h5grove==1.3.0 ; python_version >= "3.7" and python_version < "3.12" -h5py==3.8.0 ; python_version >= "3.7" and python_version < "3.12" -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" -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" -jsonref==1.1.0 ; python_version >= "3.7" and python_version < "3.12" -jsonschema==4.17.3 ; python_version >= "3.7" and python_version < "3.12" -kombu==5.2.4 ; python_version >= "3.7" and python_version < "3.12" -lagom==2.4.1 ; python_version >= "3.7" and python_version < "3.12" -lxml==4.9.3 ; python_version >= "3.7" and python_version < "3.12" -mako==1.2.4 ; python_version >= "3.7" and python_version < "3.12" -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" -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" -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" +a2wsgi==1.9.0 ; python_version >= "3.8" and python_version < "3.12" +adal==1.2.7 ; python_version >= "3.8" and python_version < "3.12" +aiobotocore==2.9.0 ; python_version >= "3.8" and python_version < "3.12" +aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.12" +aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.12" +aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.12" +aioitertools==0.11.0 ; python_version >= "3.8" and python_version < "3.12" +aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.12" +alembic==1.13.1 ; python_version >= "3.8" and python_version < "3.12" +amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.12" +aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.12" +anyio==4.2.0 ; python_version >= "3.8" and python_version < "3.12" +apispec==6.3.1 ; python_version >= "3.8" and python_version < "3.12" +appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.12" +arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.12" +argcomplete==3.2.1 ; python_version >= "3.8" and python_version < "3.12" +async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" +attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.12" +attrs==23.1.0 ; python_version >= "3.8" and python_version < "3.12" +babel==2.14.0 ; python_version >= "3.8" and python_version < "3.12" +backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9" +backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9" +bagit-profile==1.3.1 ; python_version >= "3.8" and python_version < "3.12" +bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.12" +bcrypt==4.1.2 ; python_version >= "3.8" and python_version < "3.12" +bdbag==1.7.1 ; python_version >= "3.8" and python_version < "3.12" +beaker==1.12.1 ; python_version >= "3.8" and python_version < "3.12" +billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.12" +bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.12" +bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.12" +boltons==23.1.1 ; python_version >= "3.8" and python_version < "3.12" +boto==2.49.0 ; python_version >= "3.8" and python_version < "3.12" +botocore==1.33.13 ; python_version >= "3.8" and python_version < "3.12" +bx-python==0.10.0 ; python_version >= "3.8" and python_version < "3.12" +cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.12" +celery==5.3.6 ; python_version >= "3.8" and python_version < "3.12" +certifi==2023.11.17 ; python_version >= "3.8" and python_version < "3.12" +cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.12" +charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.12" +cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.12" +circus==0.18.0 ; python_version >= "3.8" and python_version < "3.12" +click-didyoumean==0.3.0 ; python_version >= "3.8" and python_version < "3.12" +click-plugins==1.1.1 ; python_version >= "3.8" and python_version < "3.12" +click-repl==0.3.0 ; python_version >= "3.8" and python_version < "3.12" +click==8.1.7 ; python_version >= "3.8" and python_version < "3.12" +cloudauthz==0.6.0 ; python_version >= "3.8" and python_version < "3.12" +cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.12" +colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.12" and platform_system == "Windows" +coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.12" +conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.12" +cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.12" +cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.12" +cwl-utils==0.32 ; python_version >= "3.8" and python_version < "3.12" +cwltool==3.1.20231207110929 ; python_version >= "3.8" and python_version < "3.12" +decorator==5.1.1 ; python_version >= "3.8" and python_version < "3.12" +defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.12" +deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.12" +dictobj==0.4 ; python_version >= "3.8" and python_version < "3.12" +dnspython==2.4.2 ; python_version >= "3.8" and python_version < "3.12" +docopt==0.6.2 ; python_version >= "3.8" and python_version < "3.12" +docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.12" +dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.12" +ecdsa==0.18.0 ; python_version >= "3.8" and python_version < "3.12" +edam-ontology==1.25.2 ; python_version >= "3.8" and python_version < "3.12" +email-validator==2.1.0.post1 ; python_version >= "3.8" and python_version < "3.12" +exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11" +fastapi==0.98.0 ; python_version >= "3.8" and python_version < "3.12" +filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.12" +frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.12" +fs==2.4.16 ; python_version >= "3.8" and python_version < "3.12" +fsspec==2023.12.2 ; python_version >= "3.8" and python_version < "3.12" +future==0.18.3 ; python_version >= "3.8" and python_version < "3.12" +galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.12" +galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.12" +graphene-sqlalchemy==3.0.0rc1 ; python_version >= "3.8" and python_version < "3.12" +graphene==3.3 ; python_version >= "3.8" and python_version < "3.12" +graphql-core==3.2.3 ; python_version >= "3.8" and python_version < "3.12" +graphql-relay==3.2.0 ; python_version >= "3.8" and python_version < "3.12" +gravity==1.0.4 ; python_version >= "3.8" and python_version < "3.12" +greenlet==3.0.1 ; python_version >= "3.8" 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 >= "3.8" and python_version < "3.12" +gxformat2==0.18.0 ; python_version >= "3.8" and python_version < "3.12" +h11==0.14.0 ; python_version >= "3.8" and python_version < "3.12" +h5grove==1.3.0 ; python_version >= "3.8" and python_version < "3.12" +h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.12" +humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.12" +idna==3.6 ; python_version >= "3.8" and python_version < "3.12" +importlib-metadata==7.0.1 ; python_version >= "3.8" and python_version < "3.12" +importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.9" +isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.12" +isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.12" +jinja2==3.1.2 ; python_version >= "3.8" and python_version < "3.12" +jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.12" +jsonref==1.1.0 ; python_version >= "3.8" and python_version < "3.12" +jsonschema-specifications==2023.11.2 ; python_version >= "3.8" and python_version < "3.12" +jsonschema==4.20.0 ; python_version >= "3.8" and python_version < "3.12" +kombu==5.3.4 ; python_version >= "3.8" and python_version < "3.12" +lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.12" +lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.12" +mako==1.3.0 ; python_version >= "3.8" and python_version < "3.12" +markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.12" +markdown==3.5.1 ; python_version >= "3.8" and python_version < "3.12" +markupsafe==2.1.3 ; python_version >= "3.8" and python_version < "3.12" +mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.12" +mercurial==6.6.1 ; python_version >= "3.8" and python_version < "3.12" +mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.12" +mrcfile==1.4.3 ; python_version >= "3.8" and python_version < "3.12" +msal==1.26.0 ; python_version >= "3.8" and python_version < "3.12" +msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.12" +multidict==6.0.4 ; python_version >= "3.8" and python_version < "3.12" +mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.12" +networkx==2.5 ; python_version >= "3.8" and python_version < "3.12" +nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "3.12" 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" -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" -parsley==1.3 ; python_version >= "3.7" and python_version < "3.12" -paste==3.5.3 ; python_version >= "3.7" and python_version < "3.12" -pastedeploy==3.0.1 ; python_version >= "3.7" and python_version < "3.12" -pebble==5.0.3 ; python_version >= "3.7" and python_version < "3.12" -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" -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" -pydantic-tes==0.1.5 ; python_version >= "3.7" and python_version < "3.12" -pydantic==2.1.1 ; python_version >= "3.7" and python_version < "3.12" -pydantic_core==2.4.0 ; python_version >= "3.7" and python_version < "3.12" -pydot==1.4.2 ; python_version >= "3.7" and python_version < "3.12" -pyeventsystem==0.1.0 ; python_version >= "3.7" and python_version < "3.12" -pyfaidx==0.7.2.1 ; python_version >= "3.7" and python_version < "3.12" -pygments==2.16.1 ; python_version >= "3.7" and python_version < "3.12" -pyjwt==2.8.0 ; python_version >= "3.7" and python_version < "3.12" -pyjwt[crypto]==2.8.0 ; python_version >= "3.7" and python_version < "3.12" -pykwalify==1.8.0 ; python_version >= "3.7" and python_version < "3.12" -pylibmagic==0.4.0 ; python_version >= "3.7" and python_version < "3.12" -pynacl==1.5.0 ; python_version >= "3.7" and python_version < "3.12" -pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12" +numpy==1.26.2 ; python_version >= "3.9" and python_version < "3.12" +oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.12" +orjson==3.9.10 ; python_version >= "3.8" and python_version < "3.12" +oyaml==1.0 ; python_version >= "3.8" and python_version < "3.12" +packaging==23.2 ; python_version >= "3.8" and python_version < "3.12" +paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.12" +parsley==1.3 ; python_version >= "3.8" and python_version < "3.12" +paste==3.7.1 ; python_version >= "3.8" and python_version < "3.12" +pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.12" +pebble==5.0.5 ; python_version >= "3.8" and python_version < "3.12" +pkgutil-resolve-name==1.3.10 ; python_version >= "3.8" and python_version < "3.9" +promise==2.3 ; python_version >= "3.8" and python_version < "3.12" +prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.12" +prov==1.5.1 ; python_version >= "3.8" and python_version < "3.12" +psutil==5.9.7 ; python_version >= "3.8" and python_version < "3.12" +pulsar-galaxy-lib==0.15.5 ; python_version >= "3.8" and python_version < "3.12" +pyasn1==0.5.1 ; python_version >= "3.8" and python_version < "3.12" +pycparser==2.21 ; python_version >= "3.8" and python_version < "3.12" +pycryptodome==3.19.0 ; python_version >= "3.8" and python_version < "3.12" +pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.12" +pydantic==1.10.13 ; python_version >= "3.8" and python_version < "3.12" +pydantic[email]==1.10.13 ; python_version >= "3.8" and python_version < "3.12" +pydot==1.4.2 ; python_version >= "3.8" and python_version < "3.12" +pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.12" +pyfaidx==0.7.2.2 ; python_version >= "3.8" and python_version < "3.12" +pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.12" +pyjwt==2.8.0 ; python_version >= "3.8" and python_version < "3.12" +pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.12" +pykwalify==1.8.0 ; python_version >= "3.8" and python_version < "3.12" +pylibmagic==0.5.0 ; python_version >= "3.8" and python_version < "3.12" +pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.12" +pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.12" pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12" -pyreadline==2.1 ; sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7" -pyrsistent==0.19.3 ; python_version >= "3.7" and python_version < "3.12" -pysam==0.21.0 ; python_version >= "3.7" and python_version < "3.12" -python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12" -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" -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" -refgenconf==0.12.2 ; python_version >= "3.7" and python_version < "3.12" -repoze-lru==0.7 ; python_version >= "3.7" and python_version < "3.12" -requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.12" -requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12" -requests-unixsocket==0.3.0 ; python_version >= "3.7" and python_version < "3.12" -requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12" -rich==13.5.2 ; python_version >= "3.7" and python_version < "3.12" -rocrate==0.8.0 ; python_version >= "3.7" and python_version < "3.12" -routes==2.5.1 ; python_version >= "3.7" and python_version < "3.12" -rsa==4.9 ; python_version >= "3.7" and python_version < "3.12" -ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7" -ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12" -s3fs==2023.1.0 ; python_version >= "3.7" and python_version < "3.12" -schema-salad==8.4.20230808163024 ; python_version >= "3.7" and python_version < "3.12" -setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.12" -setuptools==68.0.0 ; python_version >= "3.7" and python_version < "3.12" -shellescape==3.8.1 ; python_version >= "3.7" and python_version < "3.12" -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" -social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.7" and python_version < "3.12" -sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.12" -sqlalchemy==1.4.49 ; python_version >= "3.7" and python_version < "3.12" -sqlitedict==2.1.0 ; python_version >= "3.7" and python_version < "3.12" -sqlparse==0.4.4 ; python_version >= "3.7" and python_version < "3.12" -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" -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" -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" -tuswsgi==0.5.5 ; python_version >= "3.7" and python_version < "3.12" -typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.12" -tzdata==2023.3 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows" -tzlocal==5.0.1 ; python_version >= "3.7" and python_version < "3.12" -ubiquerg==0.6.3 ; python_version >= "3.7" and python_version < "3.12" -urllib3==1.26.16 ; python_version >= "3.7" and python_version < "3.12" -uvicorn==0.22.0 ; python_version >= "3.7" and python_version < "3.12" -uvloop==0.17.0 ; python_version >= "3.7" and python_version < "3.12" -vine==5.0.0 ; python_version >= "3.7" and python_version < "3.12" -wcwidth==0.2.6 ; python_version >= "3.7" and python_version < "3.12" -webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.12" -webob==1.8.7 ; python_version >= "3.7" and python_version < "3.12" -whoosh==2.7.4 ; python_version >= "3.7" and python_version < "3.12" -wrapt==1.15.0 ; python_version >= "3.7" and python_version < "3.12" -yacman==0.9.1 ; python_version >= "3.7" and python_version < "3.12" -yarl==1.9.2 ; python_version >= "3.7" and python_version < "3.12" -zipp==3.15.0 ; python_version >= "3.7" and python_version < "3.12" -zipstream-new==1.1.8 ; python_version >= "3.7" and python_version < "3.12" -zstandard==0.21.0 ; python_version >= "3.7" and python_version < "3.12" +pysam==0.22.0 ; python_version >= "3.8" and python_version < "3.12" +python-dateutil==2.8.2 ; python_version >= "3.8" and python_version < "3.12" +python-jose==3.3.0 ; python_version >= "3.8" and python_version < "3.12" +python-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.12" +python-multipart==0.0.6 ; python_version >= "3.8" and python_version < "3.12" +python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.12" +pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.12" +pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.12" +pyzmq==25.1.2 ; python_version >= "3.8" and python_version < "3.12" +rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.12" +referencing==0.32.0 ; python_version >= "3.8" and python_version < "3.12" +refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.12" +regex==2023.10.3 ; python_version >= "3.8" and python_version < "3.12" +repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.12" +requests-oauthlib==1.3.1 ; python_version >= "3.8" and python_version < "3.12" +requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.12" +requests-unixsocket==0.3.0 ; python_version >= "3.8" and python_version < "3.12" +requests==2.31.0 ; python_version >= "3.8" and python_version < "3.12" +rich==13.7.0 ; python_version >= "3.8" and python_version < "3.12" +rocrate==0.9.0 ; python_version >= "3.8" and python_version < "3.12" +routes==2.5.1 ; python_version >= "3.8" and python_version < "3.12" +rpds-py==0.15.2 ; python_version >= "3.8" and python_version < "3.12" +rsa==4.9 ; python_version >= "3.8" and python_version < "3.12" +ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.12" and python_version >= "3.8" +ruamel-yaml==0.18.5 ; python_version >= "3.8" and python_version < "3.12" +s3fs==2023.12.2 ; python_version >= "3.8" and python_version < "3.12" +schema-salad==8.5.20231201181309 ; python_version >= "3.8" and python_version < "3.12" +setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.12" +setuptools==69.0.2 ; python_version >= "3.8" and python_version < "3.12" +shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.12" +six==1.16.0 ; python_version >= "3.8" and python_version < "3.12" +sniffio==1.3.0 ; python_version >= "3.8" and python_version < "3.12" +social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.8" and python_version < "3.12" +sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.12" +spython==0.3.13 ; python_version >= "3.8" and python_version < "3.12" +sqlalchemy==1.4.50 ; python_version >= "3.8" and python_version < "3.12" +sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.12" +sqlparse==0.4.4 ; python_version >= "3.8" and python_version < "3.12" +starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.12" +starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.12" +starlette==0.27.0 ; python_version >= "3.8" and python_version < "3.12" +supervisor==4.2.5 ; python_version >= "3.8" and python_version < "3.12" +svgwrite==1.4.3 ; python_version >= "3.8" and python_version < "3.12" +tenacity==8.2.3 ; python_version >= "3.8" and python_version < "3.12" +tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.12" +tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.12" +tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" +tornado==6.4 ; python_version >= "3.8" and python_version < "3.12" +tqdm==4.66.1 ; python_version >= "3.8" and python_version < "3.12" +tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.12" +tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.12" +typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.12" +tzdata==2023.3 ; python_version >= "3.8" and python_version < "3.12" +tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.12" +ubiquerg==0.6.3 ; python_version >= "3.8" and python_version < "3.12" +urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.12" +uvicorn==0.25.0 ; python_version >= "3.8" and python_version < "3.12" +uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.12" +vine==5.1.0 ; python_version >= "3.8" and python_version < "3.12" +wcwidth==0.2.12 ; python_version >= "3.8" and python_version < "3.12" +webencodings==0.5.1 ; python_version >= "3.8" and python_version < "3.12" +webob==1.8.7 ; python_version >= "3.8" and python_version < "3.12" +whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.12" +wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.12" +yacman==0.9.2 ; python_version >= "3.8" and python_version < "3.12" +yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.12" +zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.12" +zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.12" +zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index efb4c00c509..57a3f369a2c 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,22 +1,21 @@ -cffi==1.15.1 -cryptography==41.0.3 -mypy==1.4.1 -mypy-extensions==1.0.0 -pycparser==2.21 -pydantic==2.1.1 -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==1.16.0 ; python_version >= "3.8" and python_version < "3.12" +cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.12" +mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.12" +mypy==1.8.0 ; python_version >= "3.8" and python_version < "3.12" +pycparser==2.21 ; python_version >= "3.8" and python_version < "3.12" +pydantic==1.10.13 ; python_version >= "3.8" and python_version < "3.12" +tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" +types-bleach==6.1.0.1 ; python_version >= "3.8" and python_version < "3.12" +types-boto==2.49.18.9 ; python_version >= "3.8" and python_version < "3.12" +types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.12" +types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.12" +types-docutils==0.20.0.3 ; python_version >= "3.8" and python_version < "3.12" +types-markdown==3.5.0.3 ; python_version >= "3.8" and python_version < "3.12" +types-paramiko==3.3.0.2 ; python_version >= "3.8" and python_version < "3.12" +types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.12" +types-python-dateutil==2.8.19.14 ; python_version >= "3.8" and python_version < "3.12" +types-pyyaml==6.0.12.12 ; python_version >= "3.8" and python_version < "3.12" +types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.12" +types-six==1.16.21.9 ; python_version >= "3.8" and python_version < "3.12" +types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.12" +typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.12" diff --git a/pyproject.toml b/pyproject.toml index f1a9a35a2c7..619effdbb8e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,10 +1,11 @@ [tool.black] line-length = 120 -target-version = ['py37'] +target-version = ['py38'] include = '\.pyi?$' extend-exclude = ''' ^/( | packages + | lib/tool_shed/test/test_data/repos )/ ''' @@ -22,9 +23,14 @@ homepage = "https://galaxyproject.org/" repository = "https://github.com/galaxyproject/galaxy/" documentation = "https://docs.galaxyproject.org/" +[[tool.poetry.source]] +name = "PyPI" +priority = "default" + [[tool.poetry.source]] name = "galaxyproject" url = "https://wheels.galaxyproject.org/simple" +priority = "primary" [tool.poetry.dependencies] a2wsgi = "*" @@ -44,26 +50,26 @@ Cheetah3 = "!=3.2.6.post2" # yanked release, https://github.com/python-poetry/p cloudauthz = "==0.6.0" cloudbridge = "*" circus = "*" -cwltool = "==3.1.20221109155812" +cwltool = ">=3.1.20230624081518" # save time, minimum needed by cwl-1.0 branch conda-package-streaming = "*" dictobj = "*" dnspython = "*" docutils = "!=0.17, !=0.17.1" +dparse = "*" edam-ontology = "*" -fastapi = ">0.101.0" -fastapi-utils = "*" +fastapi = ">=0.71.0, !=0.89.0, <0.99" # https://github.com/tiangolo/fastapi/issues/4041 https://github.com/tiangolo/fastapi/issues/5861 fs = "*" future = "*" galaxy_sequence_utils = "*" -gravity = ">=1.0" +graphene-sqlalchemy = "3.0.0rc1" # need a beta release to be compat. with starlette plugin +gravity = ">=1.0.4" gunicorn = "*" gxformat2 = "*" h5grove = ">=1.2.1" h5py = "*" -importlib-metadata = "<5" # Work around https://github.com/celery/kombu/issues/1600 -importlib-resources = "*" -isa-rwval = "*" -kombu = "*" +importlib-resources = { version = "*", python = "<3.9" } # for importlib.{abc.Traversable,resources.{files, Package}} +isa-rwval = ">=0.10.10" +kombu = ">=5.3" # for importlib-metadata fix lagom = "*" Mako = "*" Markdown = "*" @@ -81,18 +87,19 @@ pebble = "*" psutil = "*" pulsar-galaxy-lib = ">=0.15.0.dev0" pycryptodome = "*" -pydantic = {version = ">=2", extras = ["email"]} +pydantic = {version = "<2", extras = ["email"]} PyJWT = "*" pykwalify = "*" pylibmagic = "*" -pyparsing = "<3.1" # Needed by matplotlib on Python >=3.8 https://github.com/matplotlib/matplotlib/issues/26152 +pyparsing = "*" pysam = ">=0.21" # for Python 3.11 support on macOS -python = ">=3.7,<3.12" # Keep maximum version strict to appease numpy and scipy +python = ">=3.8,<3.12" # Keep maximum version strict to appease numpy and scipy python-dateutil = "*" python-magic = "*" python-multipart = "*" # required to support form parsing in FastAPI/Starlette PyYAML = "*" refgenconf = ">=0.12.0" +regex = "*" requests = "*" rocrate = "*" Routes = "*" @@ -104,6 +111,7 @@ sqlitedict = "*" sqlparse = "*" starlette = "*" starlette-context = "*" +starlette-graphene3 = "*" svgwrite = "*" tifffile = "*" tuswsgi = "*" @@ -130,6 +138,7 @@ lxml = "!=4.2.2" markdown-it-reporter = "*" myst-parser = "*" pkce = "*" +playwright = "*" pytest = "*" pytest-asyncio = "*" pytest-celery = "*" @@ -139,28 +148,49 @@ pytest-httpserver = "*" python-irodsclient = "!=1.1.2" # https://github.com/irods/python-irodsclient/issues/356 pytest-json-report = "*" pytest-mock = "*" +pytest-playwright = "*" pytest-postgresql = "!=3.0.0" # https://github.com/ClearcodeHQ/pytest-postgresql/issues/426 pytest-shard = "*" responses = "*" selenium = "*" +urllib3 = "<2" # Necessary for poetry for resolve deps for Python 3.8+ seletools = "*" Sphinx = ">=4.0" # support docutils 0.17 -sphinx_rtd_theme = ">=1.0.0" +sphinx-rtd-theme = ">=1.0.0,<2" # https://github.com/python-poetry/poetry/issues/8194 statsd = "*" testfixtures = "*" tuspy = "*" -twill = "*" +twill = ">=3.2.1" # https://github.com/twill-tools/twill/issues/18 watchdog = "*" +[tool.poetry.group.typecheck.dependencies] +mypy = "*" +pydantic = "<2" # for pydantic.mypy plugin +types-bleach = "*" +types-boto = "*" +types-contextvars = "*" +types-dataclasses = "*" +types-docutils = "*" +types-Markdown = "*" +types-paramiko = "*" +types-pkg-resources = "*" +types-python-dateutil = "*" +types-PyYAML = "*" +types-requests = "*" +types-six = "*" + [tool.ruff] -select = ["E", "F", "B", "UP"] -target-version = "py37" +# Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B), +# flake8-logging-format (G) and pyupgrade (UP) +select = ["E", "F", "B", "G", "UP"] +target-version = "py38" # Exceptions: # B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body) # B9 flake8-bugbear opinionated warnings # E402 module level import not at top of file # TODO, we would like to improve this. # E501 is line length (delegated to black) -ignore = ["B008", "B9", "E402", "E501"] +# G* are TODOs +ignore = ["B008", "B9", "E402", "E501", "G001", "G002", "G004"] exclude = [ "lib/tool_shed/test/test_data/repos" ] @@ -178,3 +208,5 @@ relative-imports-order = "closest-to-furthest" # Don't check some pyupgrade rules on generated files "lib/galaxy/schema/bco/*" = ["UP006", "UP007"] "lib/galaxy/schema/drs/*" = ["UP006", "UP007"] +"lib/tool_shed_client/schema/trs.py" = ["UP006", "UP007"] +"lib/tool_shed_client/schema/trs_service_info.py" = ["UP006", "UP007"]