diff --git a/requirements-dev.txt b/requirements-dev.txt index 96c6876a..12d898e0 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -4,53 +4,53 @@ # # pip-compile requirements-dev.in # -aiohappyeyeballs==2.4.0 +aiohappyeyeballs==2.4.3 # via aiohttp -aiohttp==3.10.* - # via -r requirements.in +aiohttp==3.11.7 + # via -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in aiomysql==0.2.0 # via databases aiosignal==1.3.1 # via aiohttp annotated-types==0.7.0 # via pydantic -anyio==4.4.0 +anyio==4.6.2.post1 # via # httpx # starlette # watchfiles -astroid==3.2.4 +astroid==3.3.5 # via pylint async-lru==2.0.4 - # via -r requirements.in + # via -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in attrs==24.2.0 # via # aiohttp # flake8-bugbear -azure-core==1.30.2 +azure-core==1.32.0 # via # azure-storage-blob # azure-storage-file-datalake -azure-storage-blob==12.22.0 +azure-storage-blob==12.24.0 # via # azure-storage-file-datalake # cloudpathlib -azure-storage-file-datalake==12.16.0 +azure-storage-file-datalake==12.18.0 # via cloudpathlib backoff==2.2.1 - # via -r requirements.in -black==24.8.0 + # via -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in +black==24.10.0 # via -r requirements-dev.in -blinker==1.8.2 +blinker==1.9.0 # via flask -boto3==1.35.12 +boto3==1.35.70 # via - # -r requirements.in + # -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in # cloudpathlib # cpg-utils -botocore==1.35.12 +botocore==1.35.70 # via - # -r requirements.in + # -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in # boto3 # cpg-utils # s3transfer @@ -67,7 +67,7 @@ cffi==1.17.1 # via cryptography cfgv==3.4.0 # via pre-commit -charset-normalizer==3.3.2 +charset-normalizer==3.4.0 # via requests click==8.1.7 # via @@ -79,32 +79,32 @@ click==8.1.7 # uvicorn cloudevents==1.11.0 # via functions-framework -cloudpathlib[all,azure,gs,s3]==0.19.0 +cloudpathlib[all,azure,gs,s3]==0.20.0 # via - # -r requirements.in + # -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in # cpg-utils -coverage[toml]==7.6.1 +coverage[toml]==7.6.8 # via # -r requirements-dev.in # pytest-cov -cpg-utils==5.1.0 - # via -r requirements.in -cryptography==43.0.1 +cpg-utils==5.1.1 + # via -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in +cryptography==43.0.3 # via - # -r requirements.in + # -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in # azure-storage-blob # pymysql databases[mysql]==0.9.0 - # via -r requirements.in -deprecated==1.2.14 + # via -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in +deprecated==1.2.15 # via cpg-utils deprecation==2.1.0 # via cloudevents -dill==0.3.8 +dill==0.3.9 # via pylint -distlib==0.3.8 +distlib==0.3.9 # via virtualenv -dnspython==2.6.1 +dnspython==2.7.0 # via email-validator docker==7.1.0 # via testcontainers @@ -112,29 +112,29 @@ email-validator==2.2.0 # via fastapi fastapi[all]==0.115.5 # via - # -r requirements.in + # -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in # strawberry-graphql fastapi-cli[standard]==0.0.5 # via fastapi -filelock==3.15.4 +filelock==3.16.1 # via virtualenv flake8==7.1.1 # via # -r requirements-dev.in # flake8-bugbear -flake8-bugbear==24.8.19 +flake8-bugbear==24.10.31 # via -r requirements-dev.in -flask==3.0.3 +flask==3.1.0 # via functions-framework -frozendict==2.4.4 +frozendict==2.4.6 # via cpg-utils -frozenlist==1.4.1 +frozenlist==1.5.0 # via # aiohttp # aiosignal -functions-framework==3.8.1 +functions-framework==3.8.2 # via -r requirements-dev.in -google-api-core[grpc]==2.19.2 +google-api-core[grpc]==2.23.0 # via # google-cloud-appengine-logging # google-cloud-bigquery @@ -143,39 +143,39 @@ google-api-core[grpc]==2.19.2 # google-cloud-pubsub # google-cloud-secret-manager # google-cloud-storage -google-auth==2.34.0 +google-auth==2.36.0 # via - # -r requirements.in + # -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in # cpg-utils # google-api-core # google-cloud-appengine-logging # google-cloud-core # google-cloud-secret-manager # google-cloud-storage -google-cloud-appengine-logging==1.4.5 +google-cloud-appengine-logging==1.5.0 # via google-cloud-logging google-cloud-audit-log==0.3.0 # via google-cloud-logging google-cloud-bigquery==3.11.4 # via + # -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in # -r requirements-dev.in - # -r requirements.in google-cloud-core==2.4.1 # via # google-cloud-bigquery # google-cloud-logging # google-cloud-storage google-cloud-logging==2.7.0 - # via -r requirements.in + # via -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in google-cloud-pubsub==2.18.3 # via + # -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in # -r requirements-dev.in - # -r requirements.in -google-cloud-secret-manager==2.20.2 +google-cloud-secret-manager==2.21.1 # via cpg-utils google-cloud-storage==1.43.0 # via - # -r requirements.in + # -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in # cloudpathlib google-crc32c==1.6.0 # via google-resumable-media @@ -183,22 +183,22 @@ google-resumable-media==2.7.2 # via # google-cloud-bigquery # google-cloud-storage -googleapis-common-protos[grpc]==1.65.0 +googleapis-common-protos[grpc]==1.66.0 # via # google-api-core # google-cloud-audit-log # grpc-google-iam-v1 # grpcio-status -graphql-core==3.2.4 +graphql-core==3.2.5 # via strawberry-graphql -greenlet==3.0.3 +greenlet==3.1.1 # via sqlalchemy grpc-google-iam-v1==0.12.7 # via # google-cloud-logging # google-cloud-pubsub # google-cloud-secret-manager -grpcio==1.66.1 +grpcio==1.68.0 # via # google-api-core # google-cloud-bigquery @@ -216,15 +216,15 @@ h11==0.14.0 # via # httpcore # uvicorn -httpcore==1.0.5 +httpcore==1.0.7 # via httpx -httptools==0.6.1 +httptools==0.6.4 # via uvicorn httpx==0.27.2 # via fastapi -identify==2.6.0 +identify==2.6.3 # via pre-commit -idna==3.8 +idna==3.10 # via # anyio # email-validator @@ -233,7 +233,7 @@ idna==3.8 # yarl iniconfig==2.0.0 # via pytest -isodate==0.6.1 +isodate==0.7.2 # via # azure-storage-blob # azure-storage-file-datalake @@ -251,11 +251,11 @@ jmespath==1.0.1 # via # boto3 # botocore -libcst==1.4.0 +libcst==1.5.1 # via strawberry-graphql markdown-it-py==3.0.0 # via rich -markupsafe==2.1.5 +markupsafe==3.0.2 # via # jinja2 # werkzeug @@ -265,7 +265,7 @@ mccabe==0.7.0 # pylint mdurl==0.1.2 # via markdown-it-py -multidict==6.0.5 +multidict==6.1.0 # via # aiohttp # yarl @@ -275,9 +275,9 @@ nest-asyncio==1.6.0 # via -r requirements-dev.in nodeenv==1.9.1 # via pre-commit -orjson==3.10.7 +orjson==3.10.12 # via fastapi -packaging==24.1 +packaging==24.2 # via # black # deprecation @@ -286,16 +286,20 @@ packaging==24.1 # pytest pathspec==0.12.1 # via black -platformdirs==4.2.2 +platformdirs==4.3.6 # via # black # pylint # virtualenv pluggy==1.5.0 # via pytest -pre-commit==3.8.0 +pre-commit==4.0.1 # via -r requirements-dev.in -proto-plus==1.24.0 +propcache==0.2.0 + # via + # aiohttp + # yarl +proto-plus==1.25.0 # via # google-api-core # google-cloud-appengine-logging @@ -303,7 +307,7 @@ proto-plus==1.24.0 # google-cloud-logging # google-cloud-pubsub # google-cloud-secret-manager -protobuf==4.25.4 +protobuf==4.25.5 # via # google-api-core # google-cloud-appengine-logging @@ -316,26 +320,26 @@ protobuf==4.25.4 # grpc-google-iam-v1 # grpcio-status # proto-plus -pyasn1==0.6.0 +pyasn1==0.6.1 # via # pyasn1-modules # rsa -pyasn1-modules==0.4.0 +pyasn1-modules==0.4.1 # via google-auth pycodestyle==2.12.1 # via flake8 pycparser==2.22 # via cffi -pydantic==2.8.2 +pydantic==2.10.2 # via # fastapi # pydantic-extra-types # pydantic-settings -pydantic-core==2.20.1 +pydantic-core==2.27.1 # via pydantic -pydantic-extra-types==2.9.0 +pydantic-extra-types==2.10.0 # via fastapi -pydantic-settings==2.4.0 +pydantic-settings==2.6.1 # via fastapi pyflakes==3.2.0 # via flake8 @@ -343,22 +347,22 @@ pygments==2.18.0 # via # rich # strawberry-graphql -pylint==3.2.7 +pylint==3.3.1 # via -r requirements-dev.in pymysql[rsa]==1.1.1 # via # -r requirements-dev.in # aiomysql # testcontainers -pytest==8.3.2 +pytest==8.3.3 # via # -r requirements-dev.in # pytest-cov -pytest-cov==5.0.0 +pytest-cov==6.0.0 # via -r requirements-dev.in python-dateutil==2.8.2 # via - # -r requirements.in + # -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in # botocore # google-cloud-bigquery # strawberry-graphql @@ -366,11 +370,11 @@ python-dotenv==1.0.1 # via # pydantic-settings # uvicorn -python-multipart==0.0.9 +python-multipart==0.0.17 # via # fastapi # strawberry-graphql -pytz==2024.1 +pytz==2024.2 # via -r requirements-dev.in pyyaml==6.0.2 # via @@ -380,20 +384,20 @@ pyyaml==6.0.2 # uvicorn requests==2.32.3 # via - # -r requirements.in + # -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in # azure-core # cpg-utils # docker # google-api-core # google-cloud-bigquery # google-cloud-storage -rich==13.8.0 +rich==13.9.4 # via # strawberry-graphql # typer rsa==4.9 # via google-auth -s3transfer==0.10.2 +s3transfer==0.10.4 # via boto3 shellingham==1.5.4 # via typer @@ -401,39 +405,38 @@ six==1.16.0 # via # azure-core # google-cloud-storage - # isodate # python-dateutil slack-sdk==3.20.2 - # via -r requirements.in + # via -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in sniffio==1.3.1 # via # anyio # httpx -sqlalchemy==2.0.34 +sqlalchemy==2.0.36 # via # databases # testcontainers -starlette==0.41.2 +starlette==0.41.3 # via # fastapi # strawberry-graphql strawberry-graphql[debug-server,fastapi]==0.243.0 # via + # -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in # -r requirements-dev.in - # -r requirements.in tabulate==0.9.0 # via cpg-utils -testcontainers[mysql]==4.8.1 +testcontainers[mysql]==4.8.2 # via -r requirements-dev.in toml==0.10.2 # via cpg-utils tomlkit==0.13.2 # via pylint -typer==0.12.5 +typer==0.13.1 # via # fastapi-cli # strawberry-graphql -types-pymysql==1.1.0.20240524 +types-pymysql==1.1.0.20241103 # via -r requirements-dev.in typing-extensions==4.12.2 # via @@ -443,13 +446,14 @@ typing-extensions==4.12.2 # fastapi # pydantic # pydantic-core + # pydantic-extra-types # sqlalchemy # strawberry-graphql # testcontainers # typer ujson==5.10.0 # via fastapi -urllib3==2.2.2 +urllib3==2.2.3 # via # botocore # docker @@ -457,27 +461,27 @@ urllib3==2.2.2 # testcontainers uvicorn[standard]==0.29.0 # via - # -r requirements.in + # -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in # fastapi # fastapi-cli # strawberry-graphql -uvloop==0.20.0 +uvloop==0.21.0 # via uvicorn -virtualenv==20.26.3 +virtualenv==20.28.0 # via pre-commit -watchdog==5.0.2 +watchdog==6.0.0 # via functions-framework -watchfiles==0.24.0 +watchfiles==1.0.0 # via uvicorn -websockets==13.0.1 +websockets==14.1 # via uvicorn -werkzeug==3.0.6 +werkzeug==3.1.3 # via # flask # functions-framework -wrapt==1.16.0 +wrapt==1.17.0 # via # deprecated # testcontainers -yarl==1.12.* +yarl==1.18.0 # via aiohttp diff --git a/requirements.txt b/requirements.txt index 4f3e1ee7..baad60d9 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,9 +4,9 @@ # # pip-compile requirements.in # -aiohappyeyeballs==2.4.0 +aiohappyeyeballs==2.4.3 # via aiohttp -aiohttp==3.10.* +aiohttp==3.11.7 # via -r requirements.in aiomysql==0.2.0 # via databases @@ -14,7 +14,7 @@ aiosignal==1.3.1 # via aiohttp annotated-types==0.7.0 # via pydantic -anyio==4.4.0 +anyio==4.6.2.post1 # via # httpx # starlette @@ -23,24 +23,24 @@ async-lru==2.0.4 # via -r requirements.in attrs==24.2.0 # via aiohttp -azure-core==1.30.2 +azure-core==1.32.0 # via # azure-storage-blob # azure-storage-file-datalake -azure-storage-blob==12.22.0 +azure-storage-blob==12.24.0 # via # azure-storage-file-datalake # cloudpathlib -azure-storage-file-datalake==12.16.0 +azure-storage-file-datalake==12.18.0 # via cloudpathlib backoff==2.2.1 # via -r requirements.in -boto3==1.35.12 +boto3==1.35.70 # via # -r requirements.in # cloudpathlib # cpg-utils -botocore==1.35.12 +botocore==1.35.70 # via # -r requirements.in # boto3 @@ -55,27 +55,27 @@ certifi==2024.8.30 # requests cffi==1.17.1 # via cryptography -charset-normalizer==3.3.2 +charset-normalizer==3.4.0 # via requests click==8.1.7 # via # typer # uvicorn -cloudpathlib[all,azure,gs,s3]==0.19.0 +cloudpathlib[all,azure,gs,s3]==0.20.0 # via # -r requirements.in # cpg-utils -cpg-utils==5.1.0 +cpg-utils==5.1.1 # via -r requirements.in -cryptography==43.0.1 +cryptography==43.0.3 # via # -r requirements.in # azure-storage-blob databases[mysql]==0.9.0 # via -r requirements.in -deprecated==1.2.14 +deprecated==1.2.15 # via cpg-utils -dnspython==2.6.1 +dnspython==2.7.0 # via email-validator email-validator==2.2.0 # via fastapi @@ -85,13 +85,13 @@ fastapi[all]==0.115.5 # strawberry-graphql fastapi-cli[standard]==0.0.5 # via fastapi -frozendict==2.4.4 +frozendict==2.4.6 # via cpg-utils -frozenlist==1.4.1 +frozenlist==1.5.0 # via # aiohttp # aiosignal -google-api-core[grpc]==2.19.2 +google-api-core[grpc]==2.23.0 # via # google-cloud-appengine-logging # google-cloud-bigquery @@ -100,7 +100,7 @@ google-api-core[grpc]==2.19.2 # google-cloud-pubsub # google-cloud-secret-manager # google-cloud-storage -google-auth==2.34.0 +google-auth==2.36.0 # via # -r requirements.in # cpg-utils @@ -109,7 +109,7 @@ google-auth==2.34.0 # google-cloud-core # google-cloud-secret-manager # google-cloud-storage -google-cloud-appengine-logging==1.4.5 +google-cloud-appengine-logging==1.5.0 # via google-cloud-logging google-cloud-audit-log==0.3.0 # via google-cloud-logging @@ -124,7 +124,7 @@ google-cloud-logging==2.7.0 # via -r requirements.in google-cloud-pubsub==2.18.3 # via -r requirements.in -google-cloud-secret-manager==2.20.2 +google-cloud-secret-manager==2.21.1 # via cpg-utils google-cloud-storage==1.43.0 # via @@ -136,22 +136,22 @@ google-resumable-media==2.7.2 # via # google-cloud-bigquery # google-cloud-storage -googleapis-common-protos[grpc]==1.65.0 +googleapis-common-protos[grpc]==1.66.0 # via # google-api-core # google-cloud-audit-log # grpc-google-iam-v1 # grpcio-status -graphql-core==3.2.4 +graphql-core==3.2.5 # via strawberry-graphql -greenlet==3.0.3 +greenlet==3.1.1 # via sqlalchemy grpc-google-iam-v1==0.12.7 # via # google-cloud-logging # google-cloud-pubsub # google-cloud-secret-manager -grpcio==1.66.1 +grpcio==1.68.0 # via # google-api-core # google-cloud-bigquery @@ -167,20 +167,20 @@ h11==0.14.0 # via # httpcore # uvicorn -httpcore==1.0.5 +httpcore==1.0.7 # via httpx -httptools==0.6.1 +httptools==0.6.4 # via uvicorn httpx==0.27.2 # via fastapi -idna==3.8 +idna==3.10 # via # anyio # email-validator # httpx # requests # yarl -isodate==0.6.1 +isodate==0.7.2 # via # azure-storage-blob # azure-storage-file-datalake @@ -194,19 +194,23 @@ jmespath==1.0.1 # botocore markdown-it-py==3.0.0 # via rich -markupsafe==2.1.5 +markupsafe==3.0.2 # via jinja2 mdurl==0.1.2 # via markdown-it-py -multidict==6.0.5 +multidict==6.1.0 # via # aiohttp # yarl -orjson==3.10.7 +orjson==3.10.12 # via fastapi -packaging==24.1 +packaging==24.2 # via google-cloud-bigquery -proto-plus==1.24.0 +propcache==0.2.0 + # via + # aiohttp + # yarl +proto-plus==1.25.0 # via # google-api-core # google-cloud-appengine-logging @@ -214,7 +218,7 @@ proto-plus==1.24.0 # google-cloud-logging # google-cloud-pubsub # google-cloud-secret-manager -protobuf==4.25.4 +protobuf==4.25.5 # via # google-api-core # google-cloud-appengine-logging @@ -227,24 +231,24 @@ protobuf==4.25.4 # grpc-google-iam-v1 # grpcio-status # proto-plus -pyasn1==0.6.0 +pyasn1==0.6.1 # via # pyasn1-modules # rsa -pyasn1-modules==0.4.0 +pyasn1-modules==0.4.1 # via google-auth pycparser==2.22 # via cffi -pydantic==2.8.2 +pydantic==2.10.2 # via # fastapi # pydantic-extra-types # pydantic-settings -pydantic-core==2.20.1 +pydantic-core==2.27.1 # via pydantic -pydantic-extra-types==2.9.0 +pydantic-extra-types==2.10.0 # via fastapi -pydantic-settings==2.4.0 +pydantic-settings==2.6.1 # via fastapi pygments==2.18.0 # via rich @@ -260,7 +264,7 @@ python-dotenv==1.0.1 # via # pydantic-settings # uvicorn -python-multipart==0.0.9 +python-multipart==0.0.17 # via # fastapi # strawberry-graphql @@ -276,11 +280,11 @@ requests==2.32.3 # google-api-core # google-cloud-bigquery # google-cloud-storage -rich==13.8.0 +rich==13.9.4 # via typer rsa==4.9 # via google-auth -s3transfer==0.10.2 +s3transfer==0.10.4 # via boto3 shellingham==1.5.4 # via typer @@ -288,7 +292,6 @@ six==1.16.0 # via # azure-core # google-cloud-storage - # isodate # python-dateutil slack-sdk==3.20.2 # via -r requirements.in @@ -296,9 +299,9 @@ sniffio==1.3.1 # via # anyio # httpx -sqlalchemy==2.0.34 +sqlalchemy==2.0.36 # via databases -starlette==0.41.2 +starlette==0.41.3 # via fastapi strawberry-graphql[fastapi]==0.243.0 # via -r requirements.in @@ -306,7 +309,7 @@ tabulate==0.9.0 # via cpg-utils toml==0.10.2 # via cpg-utils -typer==0.12.5 +typer==0.13.1 # via fastapi-cli typing-extensions==4.12.2 # via @@ -316,12 +319,13 @@ typing-extensions==4.12.2 # fastapi # pydantic # pydantic-core + # pydantic-extra-types # sqlalchemy # strawberry-graphql # typer ujson==5.10.0 # via fastapi -urllib3==2.2.2 +urllib3==2.2.3 # via # botocore # requests @@ -330,13 +334,13 @@ uvicorn[standard]==0.29.0 # -r requirements.in # fastapi # fastapi-cli -uvloop==0.20.0 +uvloop==0.21.0 # via uvicorn -watchfiles==0.24.0 +watchfiles==1.0.0 # via uvicorn -websockets==13.0.1 +websockets==14.1 # via uvicorn -wrapt==1.16.0 +wrapt==1.17.0 # via deprecated -yarl==1.12.* +yarl==1.18.0 # via aiohttp