[R] Upgrade direct Python dependencies (#6511)

DataBiosphere · Oct 28, 2024 · 686c426 · 686c426
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diff --git a/bin/wheels/runtime/Deprecated-1.2.13-py2.py3-none-any.whl b/bin/wheels/runtime/Deprecated-1.2.13-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/Deprecated-1.2.14-py2.py3-none-any.whl b/bin/wheels/runtime/Deprecated-1.2.14-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/attrs-23.1.0-py3-none-any.whl b/bin/wheels/runtime/attrs-23.1.0-py3-none-any.whl
diff --git a/bin/wheels/runtime/attrs-24.2.0-py3-none-any.whl b/bin/wheels/runtime/attrs-24.2.0-py3-none-any.whl
diff --git a/bin/wheels/runtime/bdbag-1.6.3-py2.py3-none-any.whl b/bin/wheels/runtime/bdbag-1.6.3-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/bdbag-1.7.3-py2.py3-none-any.whl b/bin/wheels/runtime/bdbag-1.7.3-py2.py3-none-any.whl
diff --git a/...elasticsearch-7.17.9-py2.py3-none-any.whl → ...lasticsearch-7.17.12-py2.py3-none-any.whl b/...elasticsearch-7.17.9-py2.py3-none-any.whl → ...lasticsearch-7.17.12-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/elasticsearch_dsl-7.4.0-py2.py3-none-any.whl b/bin/wheels/runtime/elasticsearch_dsl-7.4.0-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/elasticsearch_dsl-7.4.1-py2.py3-none-any.whl b/bin/wheels/runtime/elasticsearch_dsl-7.4.1-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/fastavro-1.8.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/bin/wheels/runtime/fastavro-1.8.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/bin/wheels/runtime/fastavro-1.9.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/bin/wheels/runtime/fastavro-1.9.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/bin/wheels/runtime/google_api_core-2.12.0-py3-none-any.whl b/bin/wheels/runtime/google_api_core-2.12.0-py3-none-any.whl
diff --git a/bin/wheels/runtime/google_api_core-2.21.0-py3-none-any.whl b/bin/wheels/runtime/google_api_core-2.21.0-py3-none-any.whl
diff --git a/bin/wheels/runtime/google_auth-2.23.3-py2.py3-none-any.whl b/bin/wheels/runtime/google_auth-2.23.3-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/google_auth-2.34.0-py2.py3-none-any.whl b/bin/wheels/runtime/google_auth-2.34.0-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/google_cloud_bigquery-3.12.0-py2.py3-none-any.whl b/bin/wheels/runtime/google_cloud_bigquery-3.12.0-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/google_cloud_bigquery-3.13.0-py2.py3-none-any.whl b/bin/wheels/runtime/google_cloud_bigquery-3.13.0-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/http_message_signatures-0.4.4-py3-none-any.whl b/bin/wheels/runtime/http_message_signatures-0.4.4-py3-none-any.whl
diff --git a/bin/wheels/runtime/http_message_signatures-0.5.0-py3-none-any.whl b/bin/wheels/runtime/http_message_signatures-0.5.0-py3-none-any.whl
diff --git a/bin/wheels/runtime/more_itertools-10.5.0-py3-none-any.whl b/bin/wheels/runtime/more_itertools-10.5.0-py3-none-any.whl
diff --git a/bin/wheels/runtime/more_itertools-9.0.0-py3-none-any.whl b/bin/wheels/runtime/more_itertools-9.0.0-py3-none-any.whl
diff --git a/bin/wheels/runtime/msgpack-1.0.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/bin/wheels/runtime/msgpack-1.0.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/bin/wheels/runtime/msgpack-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl b/bin/wheels/runtime/msgpack-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
diff --git a/...untime/proto_plus-1.24.0-py3-none-any.whl → ...untime/proto_plus-1.25.0-py3-none-any.whl b/...untime/proto_plus-1.24.0-py3-none-any.whl → ...untime/proto_plus-1.25.0-py3-none-any.whl
diff --git a/bin/wheels/runtime/tzlocal-2.1-py2.py3-none-any.whl b/bin/wheels/runtime/tzlocal-2.1-py2.py3-none-any.whl
diff --git a/bin/wheels/runtime/tzlocal-5.2-py3-none-any.whl b/bin/wheels/runtime/tzlocal-5.2-py3-none-any.whl
diff --git a/...time/urllib3-1.26.19-py2.py3-none-any.whl → ...time/urllib3-1.26.20-py2.py3-none-any.whl b/...time/urllib3-1.26.19-py2.py3-none-any.whl → ...time/urllib3-1.26.20-py2.py3-none-any.whl
diff --git a/...s/runtime/werkzeug-3.0.3-py3-none-any.whl → ...s/runtime/werkzeug-3.0.4-py3-none-any.whl b/...s/runtime/werkzeug-3.0.3-py3-none-any.whl → ...s/runtime/werkzeug-3.0.4-py3-none-any.whl
diff --git a/requirements.all.txt b/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
 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
+botocore-stubs==1.35.49
 brotli==1.1.0
 cachetools==5.5.0
 certifi==2024.8.30
@@ -21,59 +21,57 @@ chevron==0.14.0
 click==8.1.7
 colorama==0.4.4
 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
+elasticsearch==7.17.12
+elasticsearch-dsl==7.4.1
+et_xmlfile==2.0.0
+fastavro==1.9.7
 flake8==5.0.4
 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
+jq==1.8.0
 jsonschema==4.17.3
 jsonschema-spec==0.1.6
-jwcrypto==1.5.6
 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
+more-itertools==10.5.0
 moto==4.1.13
-msgpack==1.0.7
+msgpack==1.1.0
 mypy-boto3-dynamodb==1.28.73
 mypy-boto3-ecr==1.28.45
 mypy-boto3-iam==1.28.79
@@ -84,13 +82,13 @@ 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
+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
@@ -99,47 +97,44 @@ pyasn1_modules==0.4.1
 pycodestyle==2.9.1
 pycparser==2.22
 pyflakes==2.5.0
-pygithub==1.56
+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
 requests-toolbelt==1.0.0
 requirements-parser==0.2.0+1
-responses==0.22.0
-roundrobin==0.0.4
+responses==0.25.3
 rsa==4.7.2
 s3transfer==0.7.0
 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
diff --git a/requirements.dev.trans.txt b/requirements.dev.trans.txt
@@ -1,15 +1,15 @@
 blessed==1.20.0
 blinker==1.8.2
-botocore-stubs==1.35.44
+botocore-stubs==1.35.49
 brotli==1.1.0
 click==8.1.7
 colorama==0.4.4
 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
@@ -18,11 +18,9 @@ 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
 lazy-object-proxy==1.10.0
 mccabe==0.7.0
 mypy-boto3-dynamodb==1.28.73
@@ -47,16 +45,13 @@ python-editor==1.0.4
 pyzmq==26.2.0
 readchar==4.2.0
 requests-toolbelt==1.0.0
-roundrobin==0.0.4
 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
diff --git a/requirements.dev.txt b/requirements.dev.txt
@@ -1,28 +1,28 @@
 atomicwrites==1.4.1
 awscli==1.29.63
 boto3-stubs[s3,sqs,lambda,dynamodb,iam,ecr,stepfunctions,kms]==1.28.63  # match this with the version of the `boto3` runtime dependency
-coverage==6.5.0
+coverage==7.6.4
 docker==7.1.0
 flake8==5.0.4
-gevent==23.9.1
+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
-gitpython==3.1.41
-google-api-python-client==2.103.0
-google-cloud-bigquery-reservation==1.11.3
-google-cloud-storage==2.12.0
-jq==1.3.0
-locust==2.12.2
+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]==4.1.13  # match the extras with the backends listed in AzulUnitTestCase._reset_moto
 openapi-spec-validator==0.5.1
-openpyxl==3.0.6
+openpyxl==3.1.5
 posix_ipc==1.1.1
-pygithub==1.56
-python-dxf==11.4.0
-python-gitlab==3.13.0
-pyyaml==6.0.1
-responses==0.22.0
+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
diff --git a/requirements.pip.txt b/requirements.pip.txt
@@ -1,3 +1,3 @@
-pip==23.3.2
+pip==24.0
 setuptools==70.3.0
 wheel==0.38.4
diff --git a/requirements.trans.txt b/requirements.trans.txt
@@ -16,7 +16,7 @@ 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
@@ -28,5 +28,5 @@ s3transfer==0.7.0
 setuptools-scm==5.0.2
 six==1.16.0
 typing_extensions==4.12.2
-tzlocal==2.1
+tzlocal==5.2
 wrapt==1.16.0
diff --git a/requirements.txt b/requirements.txt
@@ -1,23 +1,24 @@
-attrs==23.1.0
+attrs==24.2.0
 aws-requests-auth==0.4.3
-bdbag==1.6.3
+bdbag==1.7.3
 boto3==1.28.63  # match this with the version of the `boto3-stubs` dev dependency
 botocore==1.31.63
 chevron==0.14.0
-deprecated==1.2.13
-elasticsearch==7.17.9
-elasticsearch-dsl==7.4.0
-fastavro==1.8.2
+deprecated==1.2.14
+elasticsearch==7.17.12
+elasticsearch-dsl==7.4.1
+fastavro==1.9.7
 furl==2.1.3
-google-api-core==2.12.0
-google-auth[pyopenssl]==2.23.3
-google-cloud-bigquery==3.12.0
-http-message-signatures==0.4.4
+google-api-core==2.21.0
+google-auth[pyopenssl]==2.34.0
+# Updating the following package beyond 3.13.x > breaks test & production code
+google-cloud-bigquery==3.13.0
+http-message-signatures==0.5.0
 jmespath==1.0.1
-more-itertools==9.0.0
-msgpack==1.0.7
+more-itertools==10.5.0
+msgpack==1.1.0
 requests==2.32.2
 rsa==4.7.2  # resolve ambiguity with build-time dependency
-urllib3==1.26.19
-werkzeug==3.0.3
+urllib3==1.26.20
+werkzeug==3.0.4
 -r requirements.trans.txt