chore(deps): update all major dependencies

requirements-dev.txt

@@ -7,7 +7,7 @@
 aiohappyeyeballs==2.4.0
     # via aiohttp
 aiohttp==3.10.5
-    # via -r requirements.in
+    # via -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
 aiomysql==0.2.0
     # via databases
 aiosignal==1.3.1
@@ -22,7 +22,7 @@ anyio==4.4.0
 astroid==3.2.4
     # 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
@@ -38,19 +38,19 @@ azure-storage-blob==12.22.0
 azure-storage-file-datalake==12.16.0
     # via cloudpathlib
 backoff==2.2.1
-    # via -r requirements.in
+    # via -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
 black==24.8.0
     # via -r requirements-dev.in
 blinker==1.8.2
     # via flask
 boto3==1.35.12
     # via
-    #   -r requirements.in
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   cloudpathlib
     #   cpg-utils
 botocore==1.35.12
     # via
-    #   -r requirements.in
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   boto3
     #   cpg-utils
     #   s3transfer
@@ -81,23 +81,25 @@ cloudevents==1.11.0
     # via functions-framework
 cloudpathlib[all,azure,gs,s3]==0.19.0
     # via
-    #   -r requirements.in
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   cpg-utils
 coverage[toml]==7.6.1
     # via
     #   -r requirements-dev.in
     #   pytest-cov
 cpg-utils==5.1.0
-    # via -r requirements.in
+    # via -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
 cryptography==43.0.1
     # 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
+    # via -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
 deprecated==1.2.14
-    # via cpg-utils
+    # via
+    #   cpg-utils
+    #   opentelemetry-api
 deprecation==2.1.0
     # via cloudevents
 dill==0.3.8
@@ -112,7 +114,7 @@ email-validator==2.2.0
     # via fastapi
 fastapi[all]==0.112.2
     # via
-    #   -r requirements.in
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   strawberry-graphql
 fastapi-cli[standard]==0.0.5
     # via fastapi
@@ -145,11 +147,12 @@ google-api-core[grpc]==2.19.2
     #   google-cloud-storage
 google-auth==2.34.0
     # 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-logging
     #   google-cloud-secret-manager
     #   google-cloud-storage
 google-cloud-appengine-logging==1.4.5
@@ -158,27 +161,29 @@ 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
+google-cloud-logging==3.11.3
+    # 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
     # via cpg-utils
-google-cloud-storage==1.43.0
+google-cloud-storage==2.18.2
     # via
-    #   -r requirements.in
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   cloudpathlib
 google-crc32c==1.6.0
-    # via google-resumable-media
+    # via
+    #   google-cloud-storage
+    #   google-resumable-media
 google-resumable-media==2.7.2
     # via
     #   google-cloud-bigquery
@@ -231,6 +236,8 @@ idna==3.8
     #   httpx
     #   requests
     #   yarl
+importlib-metadata==8.4.0
+    # via opentelemetry-api
 iniconfig==2.0.0
     # via pytest
 isodate==0.6.1
@@ -275,6 +282,8 @@ nest-asyncio==1.6.0
     # via -r requirements-dev.in
 nodeenv==1.9.1
     # via pre-commit
+opentelemetry-api==1.27.0
+    # via google-cloud-logging
 orjson==3.10.7
     # via fastapi
 packaging==24.1
@@ -309,9 +318,9 @@ protobuf==4.25.4
     #   google-cloud-appengine-logging
     #   google-cloud-audit-log
     #   google-cloud-bigquery
+    #   google-cloud-logging
     #   google-cloud-pubsub
     #   google-cloud-secret-manager
-    #   google-cloud-storage
     #   googleapis-common-protos
     #   grpc-google-iam-v1
     #   grpcio-status
@@ -358,7 +367,7 @@ pytest-cov==5.0.0
     # 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
@@ -380,7 +389,7 @@ 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
@@ -400,11 +409,10 @@ shellingham==1.5.4
 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
@@ -419,8 +427,8 @@ starlette==0.38.4
     #   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
@@ -457,7 +465,7 @@ 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
@@ -481,3 +489,5 @@ wrapt==1.16.0
     #   testcontainers
 yarl==1.9.10
     # via aiohttp
+zipp==3.20.2
+    # via importlib-metadata

requirements.in

@@ -10,9 +10,9 @@ cloudpathlib
 requests
 google-auth>=2.19.0
 google-cloud-bigquery==3.11.4
-google-cloud-logging==2.7.0
+google-cloud-logging==3.11.3
 google-cloud-pubsub==2.18.3
-google-cloud-storage==1.43.0
+google-cloud-storage==2.18.2
 uvicorn==0.29.0
 fastapi[all]==0.112.2
 strawberry-graphql[fastapi]==0.243.0

requirements.txt

@@ -74,7 +74,9 @@ cryptography==43.0.1
 databases[mysql]==0.9.0
     # via -r requirements.in
 deprecated==1.2.14
-    # via cpg-utils
+    # via
+    #   cpg-utils
+    #   opentelemetry-api
 dnspython==2.6.1
     # via email-validator
 email-validator==2.2.0
@@ -107,6 +109,7 @@ google-auth==2.34.0
     #   google-api-core
     #   google-cloud-appengine-logging
     #   google-cloud-core
+    #   google-cloud-logging
     #   google-cloud-secret-manager
     #   google-cloud-storage
 google-cloud-appengine-logging==1.4.5
@@ -120,18 +123,20 @@ google-cloud-core==2.4.1
     #   google-cloud-bigquery
     #   google-cloud-logging
     #   google-cloud-storage
-google-cloud-logging==2.7.0
+google-cloud-logging==3.11.3
     # via -r requirements.in
 google-cloud-pubsub==2.18.3
     # via -r requirements.in
 google-cloud-secret-manager==2.20.2
     # via cpg-utils
-google-cloud-storage==1.43.0
+google-cloud-storage==2.18.2
     # via
     #   -r requirements.in
     #   cloudpathlib
 google-crc32c==1.6.0
-    # via google-resumable-media
+    # via
+    #   google-cloud-storage
+    #   google-resumable-media
 google-resumable-media==2.7.2
     # via
     #   google-cloud-bigquery
@@ -180,6 +185,8 @@ idna==3.8
     #   httpx
     #   requests
     #   yarl
+importlib-metadata==8.4.0
+    # via opentelemetry-api
 isodate==0.6.1
     # via
     #   azure-storage-blob
@@ -202,6 +209,8 @@ multidict==6.0.5
     # via
     #   aiohttp
     #   yarl
+opentelemetry-api==1.27.0
+    # via google-cloud-logging
 orjson==3.10.7
     # via fastapi
 packaging==24.1
@@ -220,9 +229,9 @@ protobuf==4.25.4
     #   google-cloud-appengine-logging
     #   google-cloud-audit-log
     #   google-cloud-bigquery
+    #   google-cloud-logging
     #   google-cloud-pubsub
     #   google-cloud-secret-manager
-    #   google-cloud-storage
     #   googleapis-common-protos
     #   grpc-google-iam-v1
     #   grpcio-status
@@ -287,7 +296,6 @@ shellingham==1.5.4
 six==1.16.0
     # via
     #   azure-core
-    #   google-cloud-storage
     #   isodate
     #   python-dateutil
 slack-sdk==3.20.2
@@ -340,3 +348,5 @@ wrapt==1.16.0
     # via deprecated
 yarl==1.9.10
     # via aiohttp
+zipp==3.20.2
+    # via importlib-metadata