Upgrade direct Python dependencies (#6511)

requirements.all.txt

@@ -1,16 +1,16 @@
 atomicwrites==1.4.1
-attrs==23.1.0
+attrs==24.2.0
 aws-requests-auth==0.4.3
-awscli==1.29.63
+awscli==1.35.14
 bagit==1.8.1
 bagit-profile==1.3.1
-bdbag==1.6.3
+bdbag==1.7.3
 blessed==1.20.0
 blinker==1.8.2
-boto3==1.28.63
-boto3-stubs==1.28.63
-botocore==1.31.63
-botocore-stubs==1.35.44
+boto3==1.35.48
+boto3-stubs==1.35.48
+botocore==1.35.48
+botocore-stubs==1.35.50
 brotli==1.1.0
 cachetools==5.5.0
 certifi==2024.8.30
@@ -19,127 +19,124 @@ chalice==1.30.0+12
 charset-normalizer==3.4.0
 chevron==0.14.0
 click==8.1.7
-colorama==0.4.4
+colorama==0.4.6
 configargparse==1.7
-coverage==6.5.0
+coverage==7.6.4
 cryptography==43.0.3
-deprecated==1.2.13
+deprecated==1.2.14
 docker==7.1.0
 docutils==0.16
-elasticsearch==7.17.9
-elasticsearch-dsl==7.4.0
-et-xmlfile==1.1.0
-fastavro==1.8.2
-flake8==5.0.4
+elasticsearch==7.17.12
+elasticsearch-dsl==7.4.1
+et_xmlfile==2.0.0
+fastavro==1.9.7
+flake8==7.1.1
 flask==3.0.3
-flask-basicauth==0.2.0
 flask-cors==5.0.0
+flask-login==0.6.3
 furl==2.1.3
-gevent==23.9.1
+gevent==24.10.2
 geventhttpclient==2.3.1
 gitdb==4.0.11
-gitpython==3.1.41
-google-api-core==2.12.0
-google-api-python-client==2.103.0
-google-auth==2.23.3
+gitpython==3.1.43
+google-api-core==2.21.0
+google-api-python-client==2.149.0
+google-auth==2.34.0
 google-auth-httplib2==0.2.0
-google-cloud-bigquery==3.12.0
-google-cloud-bigquery-reservation==1.11.3
+google-cloud-bigquery==3.13.0
+google-cloud-bigquery-reservation==1.13.5
 google-cloud-core==2.4.1
-google-cloud-storage==2.12.0
+google-cloud-storage==2.18.2
 google-crc32c==1.6.0
 google-resumable-media==2.7.2
 googleapis-common-protos==1.65.0
 greenlet==3.1.1
 grpcio==1.67.0
 grpcio-status==1.62.3
-http-message-signatures==0.4.4
+http-message-signatures==0.5.0
 http_sfv==0.9.9
 httplib2==0.22.0
 idna==3.10
-importlib-resources==5.13.0
 inquirer==2.10.1
 itsdangerous==2.2.0
-jdcal==1.4.1
 jinja2==3.1.4
 jmespath==1.0.1
-jq==1.3.0
-jsonschema==4.17.3
-jsonschema-spec==0.1.6
-jwcrypto==1.5.6
+jq==1.8.0
+jsonschema==4.23.0
+jsonschema-path==0.3.3
+jsonschema-specifications==2023.12.1
 lazy-object-proxy==1.10.0
-locust==2.12.2
+locust==2.32.0
 markupsafe==3.0.2
 mccabe==0.7.0
-more-itertools==9.0.0
-moto==4.1.13
-msgpack==1.0.7
-mypy-boto3-dynamodb==1.28.73
-mypy-boto3-ecr==1.28.45
-mypy-boto3-iam==1.28.79
-mypy-boto3-kms==1.28.37
-mypy-boto3-lambda==1.28.83
-mypy-boto3-s3==1.28.55
-mypy-boto3-sqs==1.28.82
-mypy-boto3-stepfunctions==1.28.36
-openapi-schema-validator==0.3.4
-openapi-spec-validator==0.5.1
-openpyxl==3.0.6
+more-itertools==10.5.0
+moto==5.0.18
+msgpack==1.1.0
+mypy-boto3-dynamodb==1.35.24
+mypy-boto3-ecr==1.35.21
+mypy-boto3-iam==1.35.0
+mypy-boto3-kms==1.35.0
+mypy-boto3-lambda==1.35.49
+mypy-boto3-s3==1.35.46
+mypy-boto3-sqs==1.35.0
+mypy-boto3-stepfunctions==1.35.46
+openapi-schema-validator==0.6.2
+openapi-spec-validator==0.7.1
+openpyxl==3.1.5
 orderedmultidict==1.0.1
 packaging==24.1
 pathable==0.4.3
-pip==23.3.2
+pip==24.0
 posix_ipc==1.1.1
-proto-plus==1.24.0
+proto-plus==1.25.0
 protobuf==4.25.5
 psutil==6.1.0
-py-partiql-parser==0.3.3
+py-partiql-parser==0.5.6
 pyasn1==0.6.1
 pyasn1_modules==0.4.1
-pycodestyle==2.9.1
+pycodestyle==2.12.1
 pycparser==2.22
-pyflakes==2.5.0
-pygithub==1.56
+pyflakes==3.2.0
+pygithub==2.4.0
 pyjwt==2.9.0
 pynacl==1.5.0
 pyopenssl==24.2.1
 pyparsing==3.2.0
-pyrsistent==0.20.0
 python-dateutil==2.9.0.post0
-python-dxf==11.4.0
+python-dxf==12.1.0
 python-editor==1.0.4
-python-gitlab==3.13.0
+python-gitlab==4.13.0
 pytz==2024.2
-pyyaml==6.0.1
+pyyaml==6.0.2
 pyzmq==26.2.0
 readchar==4.2.0
-requests==2.32.2
+referencing==0.35.1
+requests==2.32.3
 requests-toolbelt==1.0.0
 requirements-parser==0.2.0+1
-responses==0.22.0
-roundrobin==0.0.4
+responses==0.25.3
+rfc3339-validator==0.1.4
+rpds-py==0.20.0
 rsa==4.7.2
-s3transfer==0.7.0
+s3transfer==0.10.3
 setuptools==70.3.0
 setuptools-scm==5.0.2
 six==1.16.0
 smmap==5.0.1
 strict-rfc3339==0.7
-toml==0.10.2
-tqdm==4.66.5
-types-awscrt==0.22.0
+tqdm==4.66.6
+types-awscrt==0.23.0
 types-s3transfer==0.10.3
-types-toml==0.10.8.20240310
 typing_extensions==4.12.2
-tzlocal==2.1
+tzlocal==5.2
 uritemplate==4.1.1
-urllib3==1.26.19
-watchdog==2.1.9
+urllib3==1.26.20
+watchdog==5.0.3
 wcwidth==0.2.13
-werkzeug==3.0.3
+werkzeug==3.0.4
 wheel==0.38.4
 wrapt==1.16.0
 www-authenticate==0.9.2
 xmltodict==0.14.2
 zope.event==5.0
-zope.interface==7.1.0
+zope.interface==7.1.1

requirements.dev.trans.txt

@@ -1,62 +1,59 @@
 blessed==1.20.0
 blinker==1.8.2
-botocore-stubs==1.35.44
+botocore-stubs==1.35.50
 brotli==1.1.0
 click==8.1.7
-colorama==0.4.4
+colorama==0.4.6
 configargparse==1.7
 docutils==0.16
-et-xmlfile==1.1.0
+et_xmlfile==2.0.0
 flask==3.0.3
-flask-basicauth==0.2.0
 flask-cors==5.0.0
+flask-login==0.6.3
 geventhttpclient==2.3.1
 gitdb==4.0.11
 google-auth-httplib2==0.2.0
 greenlet==3.1.1
 httplib2==0.22.0
-importlib-resources==5.13.0
 inquirer==2.10.1
 itsdangerous==2.2.0
-jdcal==1.4.1
 jinja2==3.1.4
-jsonschema==4.17.3
-jsonschema-spec==0.1.6
-jwcrypto==1.5.6
+jsonschema==4.23.0
+jsonschema-path==0.3.3
+jsonschema-specifications==2023.12.1
 lazy-object-proxy==1.10.0
 mccabe==0.7.0
-mypy-boto3-dynamodb==1.28.73
-mypy-boto3-ecr==1.28.45
-mypy-boto3-iam==1.28.79
-mypy-boto3-kms==1.28.37
-mypy-boto3-lambda==1.28.83
-mypy-boto3-s3==1.28.55
-mypy-boto3-sqs==1.28.82
-mypy-boto3-stepfunctions==1.28.36
-openapi-schema-validator==0.3.4
+mypy-boto3-dynamodb==1.35.24
+mypy-boto3-ecr==1.35.21
+mypy-boto3-iam==1.35.0
+mypy-boto3-kms==1.35.0
+mypy-boto3-lambda==1.35.49
+mypy-boto3-s3==1.35.46
+mypy-boto3-sqs==1.35.0
+mypy-boto3-stepfunctions==1.35.46
+openapi-schema-validator==0.6.2
 pathable==0.4.3
 psutil==6.1.0
-py-partiql-parser==0.3.3
-pycodestyle==2.9.1
-pyflakes==2.5.0
+py-partiql-parser==0.5.6
+pycodestyle==2.12.1
+pyflakes==3.2.0
 pyjwt==2.9.0
 pynacl==1.5.0
 pyparsing==3.2.0
-pyrsistent==0.20.0
 python-editor==1.0.4
 pyzmq==26.2.0
 readchar==4.2.0
+referencing==0.35.1
 requests-toolbelt==1.0.0
-roundrobin==0.0.4
+rfc3339-validator==0.1.4
+rpds-py==0.20.0
 smmap==5.0.1
-toml==0.10.2
-tqdm==4.66.5
-types-awscrt==0.22.0
+tqdm==4.66.6
+types-awscrt==0.23.0
 types-s3transfer==0.10.3
-types-toml==0.10.8.20240310
 uritemplate==4.1.1
 wcwidth==0.2.13
 www-authenticate==0.9.2
 xmltodict==0.14.2
 zope.event==5.0
-zope.interface==7.1.0
+zope.interface==7.1.1

requirements.dev.txt

@@ -1,28 +1,28 @@
 atomicwrites==1.4.1
-awscli==1.29.63
-git+https://github.com/DataBiosphere/[email protected]+12#egg=chalice
-coverage==6.5.0
+awscli==1.35.14
+boto3-stubs[s3,sqs,lambda,dynamodb,iam,ecr,stepfunctions,kms]==1.35.48  # match this with the version of the `boto3` runtime dependency
+coverage==7.6.4
 docker==7.1.0
-flake8==5.0.4
-gevent==23.9.1
-gitpython==3.1.41
-google-api-python-client==2.103.0
-google-cloud-storage==2.12.0
-google-cloud-bigquery-reservation==1.11.3
-jq==1.3.0
-locust==2.12.2
-moto[s3,sqs,sns,dynamodb,iam]==4.1.13  # match the extras with the backends listed in AzulUnitTestCase._reset_moto
-boto3-stubs[s3,sqs,lambda,dynamodb,iam,ecr,stepfunctions,kms]==1.28.63  # match this with the version of the `boto3` runtime dependency
-openapi-spec-validator==0.5.1
-openpyxl==3.0.6
-posix_ipc==1.1.1
-pygithub==1.56
-python-dxf==11.4.0
-python-gitlab==3.13.0
-pyyaml==6.0.1
+flake8==7.1.1
+gevent==24.10.2
+git+https://github.com/DataBiosphere/[email protected]+12#egg=chalice
 git+https://github.com/hannes-ucsc/[email protected]+1#egg=requirements-parser
-responses==0.22.0
+gitpython==3.1.43
+google-api-python-client==2.149.0
+google-cloud-bigquery-reservation==1.13.5
+google-cloud-storage==2.18.2
+jq==1.8.0
+locust==2.32.0
+moto[s3,sqs,sns,dynamodb,iam]==5.0.18  # match the extras with the backends listed in AzulUnitTestCase._reset_moto
+openapi-spec-validator==0.7.1
+openpyxl==3.1.5
+posix_ipc==1.1.1
+pygithub==2.4
+python-dxf==12.1.0
+python-gitlab==4.13.0
+pyyaml==6.0.2
+responses==0.25.3
 strict-rfc3339==0.7
-watchdog==2.1.9
+watchdog==5.0.3
 -r requirements.dev.trans.txt
 -r requirements.txt

requirements.pip.txt

@@ -1,3 +1,3 @@
-pip==23.3.2
+pip==24.0
 setuptools==70.3.0
 wheel==0.38.4

requirements.trans.txt

@@ -16,17 +16,17 @@ idna==3.10
 markupsafe==3.0.2
 orderedmultidict==1.0.1
 packaging==24.1
-proto-plus==1.24.0
+proto-plus==1.25.0
 protobuf==4.25.5
 pyasn1==0.6.1
 pyasn1_modules==0.4.1
 pycparser==2.22
 pyopenssl==24.2.1
 python-dateutil==2.9.0.post0
 pytz==2024.2
-s3transfer==0.7.0
+s3transfer==0.10.3
 setuptools-scm==5.0.2
 six==1.16.0
 typing_extensions==4.12.2
-tzlocal==2.1
+tzlocal==5.2
 wrapt==1.16.0