[R] Update direct Python dependencies (#6833)

requirements.all.txt

@@ -1,16 +1,16 @@
 atomicwrites==1.4.1
-attrs==24.3.0
+attrs==25.1.0
 aws-requests-auth==0.4.3
-awscli==1.37.5
+awscli==1.37.14
 bagit==1.8.1
 bagit-profile==1.3.1
 bdbag==1.7.3
 blessed==1.20.0
 blinker==1.9.0
-boto3==1.36.5
-boto3-stubs-lite==1.36.5
-botocore==1.36.5
-botocore-stubs==1.36.11
+boto3==1.36.14
+boto3-stubs-lite==1.36.14
+botocore==1.36.14
+botocore-stubs==1.36.14
 brotli==1.1.0
 cachetools==5.5.1
 certifi==2025.1.31
@@ -23,7 +23,7 @@ colorama==0.4.6
 configargparse==1.7
 coverage==7.6.10
 cryptography==44.0.0
-deprecated==1.2.15
+deprecated==1.2.18
 docker==7.1.0
 docutils==0.16
 editor==1.6.6
@@ -40,14 +40,14 @@ gevent==24.11.1
 geventhttpclient==2.3.3
 gitdb==4.0.12
 gitpython==3.1.44
-google-api-core==2.24.0
-google-api-python-client==2.159.0
+google-api-core==2.24.1
+google-api-python-client==2.160.0
 google-auth==2.38.0
 google-auth-httplib2==0.2.0
 google-cloud-bigquery==3.13.0
 google-cloud-bigquery-reservation==1.15.0
 google-cloud-core==2.4.1
-google-cloud-storage==2.19.0
+google-cloud-storage==3.0.0
 google-crc32c==1.6.0
 google-resumable-media==2.7.2
 googleapis-common-protos==1.66.0
@@ -67,20 +67,20 @@ jsonschema==4.23.0
 jsonschema-path==0.3.4
 jsonschema-specifications==2024.10.1
 lazy-object-proxy==1.10.0
-locust==2.32.6
+locust==2.32.8
 markupsafe==3.0.2
 mccabe==0.7.0
 more-itertools==10.6.0
-moto==5.0.27
+moto==5.0.28
 msgpack==1.1.0
-mypy==1.14.1
+mypy==1.15.0
 mypy-boto3-apigateway==1.36.0
 mypy-boto3-cloudwatch==1.36.0
 mypy-boto3-dynamodb==1.36.0
 mypy-boto3-ec2==1.36.8
 mypy-boto3-ecr==1.36.10
 mypy-boto3-es==1.36.0
-mypy-boto3-iam==1.36.0
+mypy-boto3-iam==1.36.13
 mypy-boto3-kms==1.36.0
 mypy-boto3-lambda==1.36.0
 mypy-boto3-s3==1.36.9
@@ -116,7 +116,7 @@ pyopenssl==25.0.0
 pyparsing==3.2.1
 python-dateutil==2.9.0.post0
 python-dxf==12.1.0
-python-gitlab==5.3.1
+python-gitlab==5.6.0
 pytz==2025.1
 pyyaml==6.0.2
 pyzmq==26.2.1

requirements.dev.trans.txt

@@ -1,6 +1,6 @@
 blessed==1.20.0
 blinker==1.9.0
-botocore-stubs==1.36.11
+botocore-stubs==1.36.14
 brotli==1.1.0
 click==8.1.8
 colorama==0.4.6
@@ -30,7 +30,7 @@ mypy-boto3-dynamodb==1.36.0
 mypy-boto3-ec2==1.36.8
 mypy-boto3-ecr==1.36.10
 mypy-boto3-es==1.36.0
-mypy-boto3-iam==1.36.0
+mypy-boto3-iam==1.36.13
 mypy-boto3-kms==1.36.0
 mypy-boto3-lambda==1.36.0
 mypy-boto3-s3==1.36.9

requirements.dev.txt

@@ -1,26 +1,26 @@
 atomicwrites==1.4.1
-awscli==1.37.5
-boto3-stubs-lite[apigateway,cloudwatch,dynamodb,ec2,ecr,es,iam,kms,lambda,s3,secretsmanager,securityhub,sns,sqs,ssm,stepfunctions,sts]==1.36.5  # match this with the version of the `boto3` runtime dendency
+awscli==1.37.14
+boto3-stubs-lite[apigateway,cloudwatch,dynamodb,ec2,ecr,es,iam,kms,lambda,s3,secretsmanager,securityhub,sns,sqs,ssm,stepfunctions,sts]==1.36.14  # match this with the version of the `boto3` runtime dendency
 coverage==7.6.10
 docker==7.1.0
 flake8==7.1.1
 gevent==24.11.1
 git+https://github.com/DataBiosphere/[email protected]+16#egg=chalice
 git+https://github.com/hannes-ucsc/[email protected]+1#egg=requirements-parser
 gitpython==3.1.44
-google-api-python-client==2.159.0
+google-api-python-client==2.160.0
 google-cloud-bigquery-reservation==1.15.0
-google-cloud-storage==2.19.0
+google-cloud-storage==3.0.0
 jq==1.8.0
-locust==2.32.6
-moto[s3,sqs,sns,dynamodb,iam]==5.0.27  # match the extras with the backends listed in AzulUnitTestCase._reset_moto
-mypy==1.14.1
+locust==2.32.8
+moto[s3,sqs,sns,dynamodb,iam]==5.0.28  # match the extras with the backends listed in AzulUnitTestCase._reset_moto
+mypy==1.15.0
 openapi-spec-validator==0.7.1
 openpyxl==3.1.5
 posix_ipc==1.1.1
 pygithub==2.5
 python-dxf==12.1.0
-python-gitlab==5.3.1
+python-gitlab==5.6.0
 pyyaml==6.0.2
 responses==0.25.6
 strict-rfc3339==0.7

requirements.txt

@@ -1,15 +1,15 @@
-attrs==24.3.0
+attrs==25.1.0
 aws-requests-auth==0.4.3
 bdbag==1.7.3
-boto3==1.36.5  # Match version of the `boto3-stubs` dev dependency
-botocore==1.36.5
+boto3==1.36.14  # Match version of the `boto3-stubs` dev dependency
+botocore==1.36.14
 chevron==0.14.0  # Match with types-chevron in requirements.dev.txt
-deprecated==1.2.15
+deprecated==1.2.18
 elasticsearch==7.17.12  # 7.x to match server-side
 elasticsearch-dsl==7.4.1  # 7.x to match server-side
 fastavro==1.10.0
 furl==2.1.3
-google-api-core==2.24.0
+google-api-core==2.24.1
 google-auth[pyopenssl]==2.38.0
 google-cloud-bigquery==3.13.0  # < 3.14.0, see https://github.com/DataBiosphere/azul/issues/6709
 http-message-signatures==0.5.0