chore(deps): update all major dependencies

requirements-dev.txt

@@ -7,7 +7,9 @@
 aiohappyeyeballs==2.4.4
     # via aiohttp
 aiohttp==3.11.11
-    # via -r requirements.in
+    # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
+    #   -r requirements.in
 aiomysql==0.2.0
     # via databases
 aiosignal==1.3.2
@@ -22,7 +24,9 @@ anyio==4.7.0
 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
+    #   -r requirements.in
 attrs==24.3.0
     # via
     #   aiohttp
@@ -38,18 +42,22 @@ azure-storage-blob==12.24.0
 azure-storage-file-datalake==12.18.0
     # via cloudpathlib
 backoff==2.2.1
-    # via -r requirements.in
+    # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
+    #   -r requirements.in
 black==24.10.0
     # via -r requirements-dev.in
 blinker==1.9.0
     # via flask
 boto3==1.35.90
     # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   -r requirements.in
     #   cloudpathlib
     #   cpg-utils
 botocore==1.35.90
     # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   -r requirements.in
     #   boto3
     #   cpg-utils
@@ -82,23 +90,31 @@ cloudevents==1.11.0
     # via functions-framework
 cloudpathlib[all,azure,gs,s3]==0.20.0
     # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   -r requirements.in
     #   cpg-utils
 coverage[toml]==7.6.10
     # via
     #   -r requirements-dev.in
     #   pytest-cov
 cpg-utils==5.2.0
-    # via -r requirements.in
+    # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
+    #   -r requirements.in
 cryptography==44.0.0
     # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   -r 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
+    #   -r requirements.in
 deprecated==1.2.15
-    # via cpg-utils
+    # via
+    #   cpg-utils
+    #   opentelemetry-api
 deprecation==2.1.0
     # via cloudevents
 dill==0.3.9
@@ -110,11 +126,14 @@ dnspython==2.7.0
 docker==7.1.0
     # via testcontainers
 duckdb==1.1.3
-    # via -r requirements.in
+    # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
+    #   -r requirements.in
 email-validator==2.2.0
     # via fastapi
 fastapi[all]==0.115.6
     # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   -r requirements.in
     #   strawberry-graphql
 fastapi-cli[standard]==0.0.7
@@ -136,7 +155,9 @@ frozenlist==1.5.0
     #   aiohttp
     #   aiosignal
 fsspec==2024.10.0
-    # via -r requirements.in
+    # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
+    #   -r requirements.in
 functions-framework==3.8.2
     # via -r requirements-dev.in
 google-api-core[grpc]==2.24.0
@@ -150,11 +171,13 @@ google-api-core[grpc]==2.24.0
     #   google-cloud-storage
 google-auth==2.37.0
     # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   -r 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==1.5.0
@@ -163,27 +186,34 @@ 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
+    #   -r 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==2.22.0
     # via cpg-utils
-google-cloud-storage==1.43.0
+google-cloud-storage==2.19.0
     # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   -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
@@ -236,6 +266,8 @@ idna==3.10
     #   httpx
     #   requests
     #   yarl
+importlib-metadata==8.5.0
+    # via opentelemetry-api
 iniconfig==2.0.0
     # via pytest
 isodate==0.7.2
@@ -280,6 +312,8 @@ nest-asyncio==1.6.0
     # via -r requirements-dev.in
 nodeenv==1.9.1
     # via pre-commit
+opentelemetry-api==1.29.0
+    # via google-cloud-logging
 orjson==3.10.12
     # via fastapi
 packaging==24.2
@@ -318,15 +352,17 @@ protobuf==4.25.5
     #   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
     #   proto-plus
 pyarrow==18.1.0
-    # via -r requirements.in
+    # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
+    #   -r requirements.in
 pyasn1==0.6.1
     # via
     #   pyasn1-modules
@@ -369,6 +405,7 @@ pytest-cov==6.0.0
     # via -r requirements-dev.in
 python-dateutil==2.8.2
     # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   -r requirements.in
     #   botocore
     #   google-cloud-bigquery
@@ -392,6 +429,7 @@ pyyaml==6.0.2
     #   uvicorn
 requests==2.32.3
     # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   -r requirements.in
     #   azure-core
     #   cpg-utils
@@ -415,10 +453,11 @@ shellingham==1.5.4
 six==1.17.0
     # via
     #   azure-core
-    #   google-cloud-storage
     #   python-dateutil
 slack-sdk==3.20.2
-    # via -r requirements.in
+    # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
+    #   -r requirements.in
 sniffio==1.3.1
     # via anyio
 sqlalchemy==2.0.36
@@ -431,6 +470,7 @@ starlette==0.41.3
     #   strawberry-graphql
 strawberry-graphql[debug-server,fastapi]==0.256.1
     # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   -r requirements-dev.in
     #   -r requirements.in
 tabulate==0.9.0
@@ -472,6 +512,7 @@ urllib3==2.3.0
     #   testcontainers
 uvicorn[standard]==0.29.0
     # via
+    #   -r /tmp/renovate/repos/github/populationgenomics/metamist/requirements.in
     #   -r requirements.in
     #   fastapi
     #   fastapi-cli
@@ -496,3 +537,5 @@ wrapt==1.17.0
     #   testcontainers
 yarl==1.18.3
     # via aiohttp
+zipp==3.21.0
+    # 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==2.19.0
 uvicorn==0.29.0
 fastapi[all]==0.115.6
 strawberry-graphql[fastapi]==0.256.1

requirements.txt

@@ -75,7 +75,9 @@ cryptography==44.0.0
 databases[mysql]==0.9.0
     # via -r requirements.in
 deprecated==1.2.15
-    # via cpg-utils
+    # via
+    #   cpg-utils
+    #   opentelemetry-api
 dnspython==2.7.0
     # via email-validator
 duckdb==1.1.3
@@ -112,6 +114,7 @@ google-auth==2.37.0
     #   google-api-core
     #   google-cloud-appengine-logging
     #   google-cloud-core
+    #   google-cloud-logging
     #   google-cloud-secret-manager
     #   google-cloud-storage
 google-cloud-appengine-logging==1.5.0
@@ -125,18 +128,20 @@ 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==2.22.0
     # via cpg-utils
-google-cloud-storage==1.43.0
+google-cloud-storage==2.19.0
     # 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
@@ -185,6 +190,8 @@ idna==3.10
     #   httpx
     #   requests
     #   yarl
+importlib-metadata==8.5.0
+    # via opentelemetry-api
 isodate==0.7.2
     # via
     #   azure-storage-blob
@@ -207,6 +214,8 @@ multidict==6.1.0
     # via
     #   aiohttp
     #   yarl
+opentelemetry-api==1.29.0
+    # via google-cloud-logging
 orjson==3.10.14
     # via fastapi
 packaging==24.2
@@ -229,9 +238,9 @@ protobuf==4.25.5
     #   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
@@ -302,7 +311,6 @@ shellingham==1.5.4
 six==1.17.0
     # via
     #   azure-core
-    #   google-cloud-storage
     #   python-dateutil
 slack-sdk==3.20.2
     # via -r requirements.in
@@ -355,3 +363,5 @@ wrapt==1.17.0
     # via deprecated
 yarl==1.18.3
     # via aiohttp
+zipp==3.21.0
+    # via importlib-metadata